Doyle was arrested Tuesday in Florida on charges of sexually preying on a detective posing as a 14-year-old girl. He is charged with more than two dozen counts relating to Internet child pornography.
Doyle's resignation was tendered through his attorney this afternoon. He is awaiting extradition to Florida.
Homeland Security Secretary Michael Chertoff said Thursday he did not believe a department official's alleged sexual misconduct resulted in a breach of national security, calling the case an individual's "misstep."
"From time to time, there will be instances when misconduct occurs," Chertoff said, referring to Doyle's arrest.
Doyle, 55, allegedly provided the pseudo-victim with his government-issued office phone and cell phone numbers, showed off his department ID and may have used his official computer in chatting her up.
"We try to weed out those who pose a security risk," Chertoff said in a briefing with reporters. "I don't know ... that background checks with people hired will predict future behavior."
But this is not the first time Doyle's alleged Internet habits have got him in trouble. A source told CBSNews.com that while working at Time magazine's Washington bureau, managers discovered that Doyle had been looking at pornography on a receptionist's computer late at night.
He admitted to the incident, was reprimanded, and was asked to give a formal apology to staffers, the source said.
The source described Doyle as friendly, well-liked and respected by the people in the Time office, who were "shocked" to learn what he'd been doing.
Doyle, who lives in suburban Silver Spring, Md., has been suspended from his job without pay and was being held without bail at a nearby detention center as Florida seeks to extradite him.